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- PDB-6ts3: EF-hands 3 and 4 of alpha-actinin in complex with CaMKII regulato... -

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Basic information

Entry
Database: PDB / ID: 6ts3
TitleEF-hands 3 and 4 of alpha-actinin in complex with CaMKII regulatory segment
Components
  • ACE-ASN-ALA-ARG-ARG-LYS-LEU-LYS-GLY-ALA-ILE-LEU-THR-THR-MET-LEU-ALA-THR-ARG-ASN-PHE
  • Alpha-actinin-2
KeywordsPEPTIDE BINDING PROTEIN / CaMKII-binding protein
Function / homology
Function and homology information


regulation of synaptic vesicle docking / actin filament uncapping / FATZ binding / titin Z domain binding / HSF1-dependent transactivation / Interferon gamma signaling / positive regulation of potassium ion transmembrane transporter activity / phospholipase C-activating angiotensin-activated signaling pathway / positive regulation of endocytic recycling / Ion transport by P-type ATPases ...regulation of synaptic vesicle docking / actin filament uncapping / FATZ binding / titin Z domain binding / HSF1-dependent transactivation / Interferon gamma signaling / positive regulation of potassium ion transmembrane transporter activity / phospholipase C-activating angiotensin-activated signaling pathway / positive regulation of endocytic recycling / Ion transport by P-type ATPases / peptidyl-threonine autophosphorylation / Unblocking of NMDA receptors, glutamate binding and activation / regulation of endocannabinoid signaling pathway / RAF activation / calcium- and calmodulin-dependent protein kinase complex / Trafficking of AMPA receptors / Ca2+ pathway / RAF/MAP kinase cascade / Ca2+/calmodulin-dependent protein kinase / negative regulation of potassium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / positive regulation of cation channel activity / LIM domain binding / microspike assembly / negative regulation of hydrolase activity / dendritic spine development / regulation of neuron migration / regulation of neurotransmitter secretion / postsynaptic actin cytoskeleton / structural constituent of postsynaptic actin cytoskeleton / positive regulation of potassium ion transport / Ion homeostasis / focal adhesion assembly / muscle cell development / positive regulation of calcium ion transport / Striated Muscle Contraction / calcium/calmodulin-dependent protein kinase activity / Nephrin family interactions / Assembly and cell surface presentation of NMDA receptors / regulation of mitochondrial membrane permeability involved in apoptotic process / cardiac muscle cell development / structural constituent of muscle / dendrite morphogenesis / sarcomere organization / cortical actin cytoskeleton / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / pseudopodium / negative regulation of potassium ion transport / regulation of neuronal synaptic plasticity / Long-term potentiation / postsynaptic density, intracellular component / glutamate receptor binding / cellular response to interferon-beta / positive regulation of cardiac muscle cell apoptotic process / cytoskeletal protein binding / titin binding / phosphatidylinositol-4,5-bisphosphate binding / Ras activation upon Ca2+ influx through NMDA receptor / platelet alpha granule lumen / response to ischemia / protein localization to plasma membrane / regulation of membrane potential / cell projection / positive regulation of receptor signaling pathway via JAK-STAT / filopodium / actin filament / postsynaptic density membrane / Schaffer collateral - CA1 synapse / Z disc / G1/S transition of mitotic cell cycle / calcium ion transport / actin filament binding / integrin binding / cell junction / Platelet degranulation / actin cytoskeleton organization / RAF/MAP kinase cascade / regulation of apoptotic process / dendritic spine / transmembrane transporter binding / cytoskeleton / calmodulin binding / postsynaptic density / cell adhesion / protein domain specific binding / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / synapse / calcium ion binding / glutamatergic synapse / mitochondrion / extracellular exosome / extracellular region / ATP binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / NTF2-like domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ACETYL GROUP / Calcium/calmodulin-dependent protein kinase type II subunit alpha / Alpha-actinin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.28 Å
AuthorsZhu, J. / Gold, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)533303 United Kingdom
CitationJournal: To Be Published
Title: EF-hands 3 and 4 of alpha-actinin in complex with CaMKII regulatory segment
Authors: Zhu, J. / Gold, M.
History
DepositionDec 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-actinin-2
B: Alpha-actinin-2
C: ACE-ASN-ALA-ARG-ARG-LYS-LEU-LYS-GLY-ALA-ILE-LEU-THR-THR-MET-LEU-ALA-THR-ARG-ASN-PHE
D: ACE-ASN-ALA-ARG-ARG-LYS-LEU-LYS-GLY-ALA-ILE-LEU-THR-THR-MET-LEU-ALA-THR-ARG-ASN-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7456
Polymers20,6574
Non-polymers882
Water4,792266
1
A: Alpha-actinin-2
C: ACE-ASN-ALA-ARG-ARG-LYS-LEU-LYS-GLY-ALA-ILE-LEU-THR-THR-MET-LEU-ALA-THR-ARG-ASN-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3733
Polymers10,3292
Non-polymers441
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-9 kcal/mol
Surface area5640 Å2
MethodPISA
2
B: Alpha-actinin-2
D: ACE-ASN-ALA-ARG-ARG-LYS-LEU-LYS-GLY-ALA-ILE-LEU-THR-THR-MET-LEU-ALA-THR-ARG-ASN-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3733
Polymers10,3292
Non-polymers441
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-9 kcal/mol
Surface area5110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.355, 47.270, 47.472
Angle α, β, γ (deg.)90.000, 110.532, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Alpha-actinin-2 / Alpha-actinin skeletal muscle isoform 2 / F-actin cross-linking protein


Mass: 7903.778 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTN2 / Production host: Escherichia coli (E. coli) / References: UniProt: P35609
#2: Protein/peptide ACE-ASN-ALA-ARG-ARG-LYS-LEU-LYS-GLY-ALA-ILE-LEU-THR-THR-MET-LEU-ALA-THR-ARG-ASN-PHE


Mass: 2424.889 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P11798*PLUS
#3: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.28→44.46 Å / Num. obs: 46303 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 16.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.038 / Net I/σ(I): 19.7
Reflection shellResolution: 1.28→1.3 Å / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2152 / CC1/2: 0.94 / Rrim(I) all: 0.487

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Processing

Software
NameVersionClassification
DIALS1.17.1_3660data collection
PHENIX1.17.1_3660refinement
DIALSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.28→44.46 Å / SU ML: 0.1249 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.6175
RfactorNum. reflection% reflection
Rfree0.1989 1996 4.32 %
Rwork0.1832 --
obs0.1839 46220 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.69 Å2
Refinement stepCycle: LAST / Resolution: 1.28→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 0 266 1618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511431
X-RAY DIFFRACTIONf_angle_d0.69821949
X-RAY DIFFRACTIONf_chiral_restr0.0699222
X-RAY DIFFRACTIONf_plane_restr0.005257
X-RAY DIFFRACTIONf_dihedral_angle_d13.0746214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.310.29581380.2523044X-RAY DIFFRACTION96.69
1.31-1.350.29071390.24273119X-RAY DIFFRACTION99.76
1.35-1.390.27231420.22973149X-RAY DIFFRACTION99.67
1.39-1.430.2451440.21273167X-RAY DIFFRACTION99.85
1.43-1.480.22141420.20523145X-RAY DIFFRACTION99.58
1.48-1.540.22621420.19783146X-RAY DIFFRACTION99.82
1.54-1.610.20031420.18813147X-RAY DIFFRACTION99.85
1.61-1.70.22291430.18883165X-RAY DIFFRACTION99.97
1.7-1.80.19321430.19453178X-RAY DIFFRACTION99.94
1.8-1.940.19821430.18963145X-RAY DIFFRACTION99.94
1.94-2.140.19111440.18063187X-RAY DIFFRACTION99.97
2.14-2.450.17451430.18193179X-RAY DIFFRACTION100
2.45-3.080.20841460.18593213X-RAY DIFFRACTION99.97
3.09-44.460.18481450.16573240X-RAY DIFFRACTION99.65
Refinement TLS params.Method: refined / Origin x: 15.1281362844 Å / Origin y: 21.9163990434 Å / Origin z: 51.1831683785 Å
111213212223313233
T0.121159552278 Å20.00884287218521 Å2-0.0138581632918 Å2-0.119212347253 Å20.0120755410377 Å2--0.156698327561 Å2
L1.04206130367 °2-0.438679642654 °2-0.297515697624 °2-0.485852111388 °2-0.0990778256617 °2--2.13401916637 °2
S0.0436904734155 Å °-0.0496646452414 Å °-0.0649457729327 Å °-0.00654105398861 Å °0.0328064869885 Å °0.0391085940183 Å °-0.0135063513924 Å °-0.289520261344 Å °-0.0432803874475 Å °
Refinement TLS groupSelection details: all

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